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<CENTER><A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A> 
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<H3>rasmol tool 
</H3>
<P><B>Purpose:</B>
</P>
<P>3d visualization via RasMol program.
</P>
<P><B>Description:</B>
</P>
<P>The rasmol tool is a wrapper on the <A HREF = "http://www.openrasmol.org">RasMol</A>
visualization program.  RasMol is open source software and runs on
many platforms.  The link above is for the Open Rasmol WWW site, not
the Protein Explorer WWW site.  Protein Explorer is a derivative of
RasMol and runs primarily on Windows machines within a browser.  This
Pizza.py tool wraps the original RasMol program, not Protein Explorer.
</P>
<P>The rasmol constructor takes a <A HREF = "pdbfile.html">pdbfile</A> object as its
argument which produces PDB files that RasMol reads in.  The pdbfile
object can produce PDB files from a LAMMPS dump or data file, as well
as in other ways.
</P>
<P>The show() method runs RasMol on the atoms of snapshot N (converted to
a PDB file) and displays the resulting image stored as image.gif.
Either a default RasMol script or one you specify is used to format
the RasMol image.  The all() method loops thru all selected snapshots
and runs RasMol on each one.  The resulting image files are saved to
image0000.gif, image0001.gif, etc.  The prefix "image" can be changed
via the file setting.
</P>
<P>A RasMol script can be created by running RasMol itself (outside of
Pizza.py), typing commands or choosing menu options to format the
display as desired, then typing "write script filename".
Alternatively the run() method will do this for you.  It runs RasMol
on snapshot N and lets you interact with RasMol directly either via
typing or mouse operations in the RasMol window.  When you type "quit"
or "exit" the script file will be saved (do not exit via the Rasmol
menu).
</P>
<P><B>Usage:</B>
</P>
<PRE>r = rasmol(p)           create RasMol wrapper for pdb object p 
</PRE>
<PRE>r.file = "image"        file prefix for created images (def = "image") 
</PRE>
<PRE>r.show(N)               show snapshot at timestep N with default script
r.show(N,"my.rasmol")   use file as RasMol script 
</PRE>
<PRE>r.all()                 make images of all selected snapshots with def script
r.all("my.rasmol")      use file as RasMol script 
</PRE>
<PRE>r.run(N)                run RasMol interactivly on snapshot N
r.run(N,"new.rasmol")                 adjust via mouse or RasMol commands
r.run(N,"new.rasmol","old.rasmol")    type quit to save RasMol script file 
</PRE>
<PRE>  if 2 args, 2nd arg is new script file, else save to "tmp.rasmol"
  if 3 args, 3rd arg is initial script file, else use default script 
</PRE>
<P><B>Related tools:</B>
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "gl.html">gl</A>, <A HREF = "pdbfile.html">pdbfile</A>,
<A HREF = "raster.html">raster</A>, <A HREF = "svg.html">svg</A>
</P>
<P><B>Prerequisites:</B>
</P>
<P>The RasMol program.
</P>
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